Genome Informatics Vol. 17_2 (2006) Presented at the 17th International Conference on Genome Informatics December 18-20, Yokohama Pacifico, Japan Published as: Y. Sakakibara, Temple F. Smith, M. Kanehisa, S. Miyano, and T. Takagi (eds.) "Genome Informatics 2006" Universal Academy Press, Tokyo, Preface by Yasubumi Sakakibara and Temple Smith Program Committee

Full Talk Papers

Hybrid Gibbs-Sampling Algorithm for Challenging Motif Discovery: GibbsDST
Kazuhito Shida
Genome Informatics 17(2): 3-13 (2006)
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Computational Annotation of Transcription Factor Binding Sites in D. Melanogaster Developmental Genes
Vipin Narang, Wing-Kin Sung, Ankush Mittal
Genome Informatics 17(2): 14-24 (2006)
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A Gram Distribution Kernel Applied to Glycan Classification and Motif Extraction
Tetsuji Kuboyama, Kouichi Hirata, Kiyoko F. Aoki-Kinoshita, Hisashi Kashima, Hiroshi Yasuda
Genome Informatics 17(2): 25-34 (2006)
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Discovering Signal Transduction Networks Using Signaling Domain-Domain Interactions
Thanh Phuong Nguyen, Tu Bao Ho
Genome Informatics 17(2): 35-45 (2006)
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Finding Conserved and Non-Conserved Reactions Using a Metabolic Pathway Alignment Algorithm
José C. Clemente, Kenji Satou, Gabriel Valiente
Genome Informatics 17(2): 46-56 (2006)
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A Function-Centric Approach to the Biological Interpretation of Microarray Time-Series
Pablo Minguez, Fátima Al-Shahrour, Joaquín Dopazo
Genome Informatics 17(2): 57-66 (2006)
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RaPiDS: An Algorithm for Rapid Expression Profile Database Search
Paul B. Horton, Larisa Kiseleva, Wataru Fujibuchi
Genome Informatics 17(2): 67-76 (2006)
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Development of an Approach for Ab Initio Estimation of Compound-Induced Liver Injury Based on Global Gene Transcriptional Profiles
Xudong Dai, Yudong D. He, Hongyue Dai, Pek Y. Lum, Christopher J. Roberts, Jeffrey F. Waring, Roger G. Ulrich
Genome Informatics 17(2): 77-88 (2006)
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The Distribution and Deposition Algorithm for Multiple Oligo Nucleotide Arrays
Kang Ning, Hon Wai Leong
Genome Informatics 17(2): 89-99 (2006)
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Detection and Restoration of Hybridization Problems in Affymetrix GeneChip Data by Parametric Scanning
Tomokazu Konishi
Genome Informatics 17(2): 100-109 (2006)
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Gene Ontology Annotation by Density and Gravitation Models
Wen-Juan Hou, Kevin Hsin-Yih Lin, Hsin-Hsi Chen
Genome Informatics 17(2): 110-120 (2006)
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Text Mining and Protein Annotations: the Construction and Use of Protein Description Sentences
Martin Krallinger, Rainer Malik, Alfonso Valencia
Genome Informatics 17(2): 121-130 (2006)
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Assessing Clustering Results with Reference Taxonomies
Gabriel Valiente
Genome Informatics 17(2): 131-140 (2006)
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Pairwise Alignment with Rearrangements
Le Sy Vinh, Andrés Varón, Ward C. Wheeler
Genome Informatics 17(2): 141-151 (2006)
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Techniques for Multi-Genome Synteny Analysis to Overcome Assembly Limitations
Arjun Bhutkar, Susan Russo, Temple F. Smith, William M. Gelbart
Genome Informatics 17(2): 152-161 (2006)
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A Markov Chain Model for Haplotype Assembly from SNP Fragments
Rui-Sheng Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen
Genome Informatics 17(2): 162-171 (2006)
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MetaClustering: Discovery of The Different Sample Clusterings in Gene Expression Data
David Venet, Hugues Bersini, Hitoshi Iba
Genome Informatics 17(2): 172-183 (2006)
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Biomarkers for Epithelial Ovarian Cancers
Pritha Mahata
Genome Informatics 17(2): 184-193 (2006)
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PepSOM: An Algorithm for Peptide Identification by Tandem Mass Spectrometry Based on SOM
Kang Ning, Hoong Kee Ng, Hon Wai Leong
Genome Informatics 17(2): 194-205 (2006)
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DAPID: A 3D-Domain Annotated Protein-Protein Interaction Database
Yung-Chiang Chen, Heng-Chu Chen, Jinn-Moon Yang
Genome Informatics 17(2): 206-215 (2006)
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A Method to Detect Important Residues Using Protein Binding Site Comparison
Keunwan Park, Dongsup Kim
Genome Informatics 17(2): 216-225 (2006)
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Modeling and Estimation of Dynamic EGFR Pathway by Data Assimilation Approach Using Time Series Proteomic Data
Shinya Tasaki, Masao Nagasaki, Masaaki Oyama, Hiroko Hata, Kazuko Ueno, Ryo Yoshida, Tomoyuki Higuchi, Sumio Sugano, Satoru Miyano
Genome Informatics 17(2): 226-238 (2006)
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A Large-Scale Computational Approach to Drug Repositioning
Yvonne Y. Li, Jianghong An, Steven J.M. Jones
Genome Informatics 17(2): 239-247 (2006)
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A Generalized Threading Model Using Integer Programming that Allows for Secondary Structure Element Deletion
Kyle Ellrott, Jun-tao Guo, Victor Olman, Ying Xu
Genome Informatics 17(2): 248-258 (2006)
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Protein Topology Classification Using Two-Stage Support Vector Machines
Jayavardhana Gubbi, Alistair Shilton, Michael Parker, Marimuthu Palaniswami
Genome Informatics 17(2): 259-269 (2006)
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Robotic Path Planning and Protein Complex Modeling Considering Low Frequency Intra-Molecular Loop and Domain Motions
Carlos A. Del Carpio, Pei Qiang, Eiichiro Ichiishi, Hideyuki Tsuboi, Michihisa Koyama, Nozomu Hatakeyama, Akira Endou, Hiromitsu Takaba, Momoji Kubo, Akira Miyamoto
Genome Informatics 17(2): 270-278 (2006)
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Keynote Address

RNAs Everywhere: Genome-Wide Annotation of Structured RNAs
Ivo L Hofacker
Genome Informatics 17(2): 281-282 (2006)
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The New Phase of Transcriptome Analysis
Yoshihide Hayashizaki
Genome Informatics 17(2): 283-283 (2006)
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Increasing Confidence of Protein-Protein Interactomes
Jin Chen, Hon Nian Chua, Wynne Hsu, Mong-Li Lee, See-Kiong Ng, Rintaro Saito, Wing-Kin Sung, Limsoon Wong
Genome Informatics 17(2): 284-297 (2006)
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